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中国农学通报

中国农学通报 ›› 2026, Vol. 42 ›› Issue (2): 50-56.doi: 10.11924/j.issn.1000-6850.casb2025-0244

• 生物科学 • 上一篇    下一篇

菘蓝基因组SSR位点分析及分子标记开发

孙天琦1(), 周蕾1, 徐林贵2, 孙晓波2, 陈勇3, 隋春1()   

  1. 1 中国医学科学院&北京协和医学院 药用植物研究所/中草药物质基础与资源利用教育部重点实验室/濒危药材繁育国家工程实验室， 北京 100193
    2 黑龙江省齐齐哈尔市泰来县农业技术推广中心， 黑龙江泰来 162400
    3 新疆农业科学院土壤肥料与农业节水研究所， 乌鲁木齐 830091
  • 收稿日期:2025-03-31 修回日期:2025-08-15 出版日期:2026-01-25 发布日期:2026-01-22
  • 通讯作者:
    隋春，女，1976年出生，吉林敦化人，研究员，博士，研究方向：药用植物种质资源评价及栽培育种。通信地址：100193 北京市海淀区马连洼北路151号 中国医学科学院药用植物研究所，Tel：010-57833363，E-mail：。
  • 作者简介:

    孙天琦，女，2001年出生，湖北襄阳人，硕士研究生，研究方向：药用植物种质资源评价及栽培育种。通信地址：100193 北京市海淀区马连洼北路151号 中国医学科学院药用植物研究所，E-mail：。

  • 基金资助:
    2024年新疆维吾尔自治区重点研发任务专项（厅地联动项目）“新疆优势特色中药材品种选育及绿色智能质控共性关键技术研究与示范”(2024B040039)

Analysis of SSR Loci and Development of Molecular Markers in Isatis indigotica Genome

SUN Tianqi1(), ZHOU Lei1, XU Lingui2, SUN Xiaobo2, CHEN Yong3, SUI Chun1()   

  1. 1 Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College / Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education / National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Beijing 100193
    2 Agricultural Technology extension Center of Tailai County, Qiqihar City, Tailai, Heilongjiang 162400
    3 Institute of Soil, Fertilizer and Agricultural Water Conservation, Xinjiang Academy of Agricultural Science, Urumqi 830091
  • Received:2025-03-31 Revised:2025-08-15 Published:2026-01-25 Online:2026-01-22

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摘要：

针对菘蓝种质鉴别缺乏有效分子标记，现有方法难以区分种内栽培类型的问题，为开发适用于菘蓝种质鉴别及遗传多样性分析的简单重复序列(simple sequence repeat，SSR)分子标记。基于菘蓝全基因组数据，利用MISA软件筛选SSR位点，通过Primer3.0设计引物，以3份栽培类型菘蓝（18个单株）为材料，验证引物的扩增稳定性、多态性、有效性及品种鉴别能力，计算遗传多样性参数。结果显示：（1）菘蓝基因组共检测到139,852个SSR位点，数目最多的单核苷酸SSR位点约占总数的72.51%，最多的SSR基序A/T，也是总核苷酸SSR基序总重复次数最高的序列，其数目为100,205次，占总重复基序的71.65%；（2）筛选出8对能够稳定扩增出基因且多态性丰富的引物，其中引物SSRSL02可用于本次供试菘蓝种质的鉴别；（3）8对引物的平均期望杂合度(He) 为0.65，Shannon’s信息指数(I)为1.34，多态性信息含量(PIC)的平均值为0.614，表明菘蓝样本具有较高的遗传多样性。综上，本研究开发的8对SSR分子标记可用于菘蓝种质资源的鉴定、遗传多样性分析和品种选育，未来可扩大菘蓝种质样本量，结合表型与有效成分含量，构建指纹图谱，为菘蓝种质资源精准评价提供更全面的技术支撑。

关键词: 菘蓝, SSR, 分子标记, 多态性, 遗传多样性, 种质资源

Abstract:

In response to the lack of effective molecular markers for the identification of Isatis indigotica germplasm and the difficulty of distinguishing cultivated types within the species using existing methods, this study aimed to develop simple sequence repeat (SSR) molecular markers suitable for germplasm identification and genetic diversity analysis in I. indigotica. Based on whole-genome data of I. indigotica, SSR loci were screened using MISA software, and primers were designed with Primer3.0. Using three cultivated types of I. indigotica (comprising 18 individual plants) as experimental materials, the amplification stability, polymorphism, effectiveness, and variety identification ability of the primers were validated. Genetic diversity parameters were also calculated. The results showed that: (1) a total of 139,852 SSR loci were detected in the I. indigotica genome. The most abundant were mononucleotide SSR loci, accounting for approximately 72.51% of the total. The most frequent SSR motif, A/T, also exhibited the highest total number of repeats among all nucleotide SSR motifs, with a count of 100,205, accounting for 71.65% of all repeated motifs. (2) Eight pairs of primers that can stably amplify genes and have rich polymorphisms were screened out. Among them, primer SSRSL02 could be used to distinguish the I. indigotica germplasms tested in this study. (3) The eight primer pairs exhibited the average expected heterozygosity (He) of 0.65, the average Shannon's information index (I) of 1.34, and the average polymorphic information content (PIC) of 0.614, indicating a relatively high level of genetic diversity within the tested I. indigotica samples. In summary, the eight SSR molecular markers developed in this study can be used for the identification of I. indigotica germplasm resources, genetic diversity analysis, and variety breeding. In the future, the sample size of I. indigotica germplasm could be expanded, and DNA fingerprinting could be constructed by integrating phenotypic data and active ingredient content, thereby providing more comprehensive technical support for the precise evaluation of I. indigotica germplasm resources.

Key words: Isatis indigotica, SSR, molecular markers, polymorphism, genetic diversity, germplasm identification